Codename: Shadow
by Aprotny
Summary: Two years have passed since Ash was saved from death by Arceus and Celebi. In those two years, war raged and Team Rocket took over. Now, Ash must go on a mission to protect the legendaries while hiding his identity from prying eyes. Meanwhile, Tracey is being held captive by Team Rocket. Possibly some shipping, but not with Ash. I don't own pokemon
1. Prologue

Ash Ketchum struggled hard as he was pushed and shoved down the halls of Team Rocket headquarters. The grunts holding him were strong and had a good grip on him, preventing him from getting away.

Agent 009, aka Domino, led the way, speaking to Giovanni on a walkie-talkie.

They reached a guarded cell and Domino motioned to the guards to move aside.

She opened the cell door and told the grunts to "throw the boy inside".

Ash was flung into the cell, where he was surprised to find his mother.

"Ash!" Delia Ketchum cried in surprise and horror.

"Mom!" Ash replied. Seeing her sorry state, he added. "What have they done to you?!"

"You have ten minutes with her, boy." Domino told him. "Say your goodbyes, because you're never going to see her again."

Ash spun around. "What?!"

Domino smirked. "Oh, don't worry about her. It's yourself you have to worry about."

Ash stared at her as the cell door was slammed shut.

Delia threw her arms around her son. "Ash!"

Ash turned and hugged her as well. He'd been so worried since Professor Juniper had told him his mother was missing. It seemed he'd had a right to worry.

They stayed like that for a few minutes before they heard the sound of Domino coming back.

"Mom, I love you. Always remember that." Ash whispered right before he was yanked away from Delia.

He resisted more as he was taken away from her, out of the cell, down the hall, up the stairs, down another hall and into a big room where Giovanni was waiting.

"What do you want?! What have you done with my mother?!" Ash shouted.

"Oh, we've had fun with her." Giovanni laughed, walking closer to the struggling boy.

Ash glared at Giovanni, angry that the man had done bad things that I will not describe here to his mother.

He felt a metal knife touch his neck and ceased his struggles immediately.

"Any last words, boy?" Giovanni sneered.

Ash fixed the evil man with another glare. "I'll stop you. That's a promise."

"Very well then." Giovanni said. He nodded to the grunt holding the knife. "Do it."

The knife ripped across Ash's neck. The boy gasped in pain. His eyes fluttered closed. He was having trouble breathing.

**Meanwhile, in a Place Far Away…**

Arceus felt Ash's death like a pain in the chest. He narrowed his eyes and roared. The chosen one couldn't die! He was still needed in the world!

**Back at Team Rocket Headquarters…**

The roar was heard throughout the facility, scratch that, throughout the world. Ash's body began to disappear.

"What's happening?" A grunt asked.

"Looks like our murder is being interfered with." Giovanni growled. "Never mind that. It's too late to save the boy now. Let them try for all I care."

**Back to Arceus…**

Arceus went quick to work with his attempts to heal Ash before it was too late. He called Celebi to aid him.

Hopefully, Ash would survive.

**(A/n) Here's the prologue of my new story. I should probably get back to work on my old ones but I'm getting writer's block for pretty much all of them. Sorry. (A/n)**


	2. Chapter 1

_(Poketalk)_

"_Telepathy"_

**Two Years Later…**

Arceus paced back and forth in the Reverse World. It had been two years since they had stopped Ash's death. TWO YEARS! Since then, many Legendary Pokemon had been captured by Team Rocket. War had erupted across the world, ending in victory on Team Rocket's side when the main armies in each region were forced to surrender. Still, there was a huge resistance against Team Rocket's rule, led by several of Ash's best friends. So far, nobody arrested by Team Rocket was ever seen again.

Giratina flew over to join Arceus. _(Impatience is not going to cause the boy to wake up any sooner, Arceus.)_

_(I know.)_ Arceus sighed. _(But the world needs him. Especially the legendries. He's protected many of us in our times of need, but now, when we need him most, all he does is sleep.)_

_(He is in a coma. He has no choice.) _Giratina pointed out. _(At least we know he will wake up eventually, Arceus. At least he's not dead.)_

_(Eventually might be too late. I must go check on my other children. The ones that remain free.)_ Arceus said. _(Take care of him. If I am not here when he wakes up, you know what to do.)_

Giratina opened a portal to allow Arceus back into the real world.

Arceus flew out. An hour later, Team Rocket ambushed him and captured him in a dark ball. **(A/n) If you do not know what a dark ball is watch Celebi: The Voice of the Forest or look on Bulbapedia. (A/n)**

**Two days later…**

Ash stirred gently and slowly opened his eyes. He blinked in confusion and pushed himself up.

"I'm… alive?" He whispered. "But… how?"

Giratina flew past him, before coming to a sudden halt and circling back.

"_You are awake."_ The legendary noted. _"That is a very good thing."_

Ash's confusion grew. "I'm… in the Reverse World? But… how? How am I alive? How am I here? How…"

"_Slow down on the questions please."_ Giratina said. _"Arceus summoned you to him when he felt you dying."_

"He…" Ash interrupted.

"_He and Celebi did their best to heal you before you faded. I'm happy to say it worked. However, you fell into a two-year coma."_ Giratina continued, stopping the boy from asking his question.

"Two _years_?! You've got to be kidding me! Everyone must think…" Again, Ash didn't get to finish.

"_Team Rocket, along with many others, believes you're dead. Arceus thinks it best to keep it that way."_ Giratina told him.

"How am I supposed to keep it that way?! I can't stay here forever!" Ash exclaimed.

"_You are only staying here a few days to regain your strength. We, Arceus and I, are sending you out on a mission. In order to complete your mission successfully, you are going to travel incognito."_ Giratina continued. _"I will explain your mission after I tell you what has happened over the past two years. It will be a lot to take in, so I suggest you lay down to conserve your strength." _ Ash nodded. He was already struggling to stay sitting up, so why not? Once Ash was laying down, Giratina continued again. _"The first event that started things rolling downhill was when Team Rocket captured the Mew from the Tree of Beginning. Do not interrupt. With Mew, they started the war, while also succeeding in capturing Regice, Registeel, Regirock, Rayquaza, Azelf, Mesprit, Uxie, Entei, Raikou, Suicune, Ho-oh, Reshiram, Meloetta, Thundurus, Landorus, and Tornadus. As far as we know, those are the only legendries captured so far. Due to having the legendries on their side, Team Rocket won the war and took over the world. Again, do not interrupt. With their new-found power, Team Rocket ordered all non-rockets to release their pokemon into the wild. Many did so out of fear, but many more formed a resistance against Team Rocket, not only to keep their pokemon, but also to regain their freedom. The resistance has tried many times to free the legendries that have already been taken, but have been unsuccessful up to this point. As for your mission, you will be going around capturing as many legendary pokemon as you can. I know this sounds wrong; however, once they are captured by you, they cannot be captured by Team Rocket. So it is your mission to do everything you can to protect them. To start off, you are going to Alto Mare. Latias's caretakers have gone to the liberty of preparing a disguise for you. They alone will know you are alive. They will help you create an alias and Latias and her children will go with you when you leave. After that, you will travel to wherever you know a legendary pokemon is residing, earn their trust, and capture them. If you have to, explain your mission to them. As a last resort, show them your face. Do you understand?"_

The information buzzed around in Ash's head for a few minutes before sinking in. He had so many things he wanted to say, but all he said was. "I understand."

"_Good. Bianca and Lorenzo know you are coming, but not when. They are prepared for whatever time you might arrive."_ Giratina said.

"And when am I arriving?" Ash asked.

"_As soon as your strength returns, which will be in a couple of days."_ Giratina replied.

Ash sighed. "I just hope my mom's okay. When I last saw her, she was Team Rocket's prisoner, and she hadn't been treated very well."

"_I know not of how your mother bides, but, for your sake, I hope she is all right." _Giratina said. _"Now rest. I have work to do."_

Ash sighed and shut his eyes, hoping his friends and family were okay.

**Meanwhile…**

"No! Don't hurt him!" Professor Oak cried as his assistant, Tracey Sketchit, was hauled away by the Team Rocket Police Force (TRPF).

The police chief stepped in front of the old man, blocking his view of the boy. "We're going to keep him alive for now, Professor, but if we hear of you giving even one scrap of supplies to the Resistance again, the child will be dead in an instant."

"Please! Leave him alone!" Professor Oak begged. "He didn't do anything wrong!"

"Oh, really? Then, tell me why we found pokeballs in his pockets." The police chief sneered. Having rendered the professor speechless, he turned around and shouted. "Take him away!" Heading to the van, he called over his shoulder. "Remember, Professor! Not one scrap!"

Professor Oak fell to his knees as the TRPF van drove away. "Tracey…"

**(A/n) Tracey will be a prominent character from now on. His experiences will be catalogued at the end of each chapter except when he is with Ash. Remember, they are happening at the same time. They are not a separate story. (A/n)**


	3. Chapter 2

**Three days later…**

Ash stepped out of a mirror in Bianca's bedroom. Fortunately, the girl wasn't in the room at the time so he didn't frighten her.

He looked around. There were painted pictures everywhere and an easel holding a pad of paper in the corner by the window. The long mirror Ash had used as a portal into the house hung on the bathroom door and a bed stood not far away.

Hearing voices, Ash exited the room. He saw some Team Rocket agents, including Annie and Oakley, standing by the front door, talking to Lorenzo and Bianca. He quickly hid before they noticed him.

"What was that?" He heard Annie say. "I thought I saw movement out of the corner of my eye."

Everyone looked to where Ash had just been. The boy had slipped back into Bianca's room in the nick of time.

"I don't see anyone." Bianca said, exchanging a glance with her grandfather. "We're not expecting anybody. Besides, even if we were, they'd probably see the Team Rocket boat parked out front and go home."

Looking around, Ash found a bag full of Master Balls, sitting on top of a cape with a hood, in the closet. There was also a mask that he soon found altered his voice. Figuring this was the disguise Lorenzo and Bianca had prepared for him, he put the mask and cape on, covering his head with the hood, grabbed the bag full of Master Balls, and jumped out the window, landing in the bushes.

He then ran through Lorenzo's workshop, into the garden.

Once in the garden, he showed his face to Latias, covered his lips with one finger, and pulled out a Master Ball to show what he wanted.

Latias had known this was coming and nodded in agreement. She convinced her three children to go inside the Master Balls first before being the last one captured.

Ash immediately called her back out and asked her to let him ride her. They had just gone out of sight when Team Rocket entered, Bianca and Lorenzo trailing behind them.

"I'm telling you! We don't have any legendary pokemon here!" Lorenzo cried.

"We all know that's a lie, Gramps." Oakley said. "We'll do this the easy way, or the hard way. Call them here now and we'll leave you be."

"But they're not here!" Bianca cried.

"Spinarak, use string shot." Oakley ordered. "Tie them to those trees."

By the time Team Rocket had searched the whole garden, Ash and the pokemon were long gone.

"Damn it! Where are those pokemon?!" Oakley shouted. She turned to Lorenzo and Bianca. "Tell us now!"

"But we don't know, Miss." Bianca said sweetly. "They must have left while we were distracting you."

"Argh! Take them to headquarters! They'll pay for this!" Oakley commanded the grunts that had come with her. "Annie and I will search this town top to bottom until we find those pokemon!"

Lorenzo and Bianca exchanged smirks as they were taken away. Looks like Ash had arrived just in time.

**Meanwhile…**

Tracey groaned as he was shoved into a cell with a woman he didn't recognize. It had been a three-day drive to Team Rocket Headquarters, which was now housed in Cameran Castle in Rota. The woman he was sharing a cell with was breast-feeding a baby that looked to be between ten and thirteen months old.

She glanced at him once when he was pushed in, before looking again at him in surprise. "Tracey?"

"Um… Do I know you?" Tracey asked, confused.

"It's me! Delia Ketchum!" The woman said.

"It is?" Tracey realized that underneath all that dirt and grime it _could_ be Mrs. Ketchum, but he still didn't recognize her. "What happened to you? And where'd the baby come from?"

"Team Rocket's leader, Giovanni… he did bad things to me, very bad things." Delia explained. "And I haven't showered in over two years. That's probably why you don't recognize me."

"So… um… what's her name?" Tracey asked, now uncomfortable.

"Hope, because she gives me hope." Delia replied quietly. "She's… all I have now… Team Rocket killed Ash and I was all alone, but now I have her and I have hope again."

"Wait a minute! Back up! Ash is _dead_?!" Tracey gasped. Delia nodded and Tracey just stared off into space. He and everyone who knew Ash had believed he'd reappear and be their savior. Now, with this new information, he felt all his hopes become crushed.

"I… I miss him…" Delia started crying. "The last thing he said to me before they took him away and killed him was to always remember that he loved me. I loved him too, but I never got to say that to him one last time. I miss him so badly. He'll never get to meet his new half-sister."

"Mama…" Hope said. "Mama…"

Delia's tear-streaked face lit up a little. "Oh! She… she said her first word!"

Tracey smiled lightly, holding back his own tears. Although Ash was gone, it was sweet to hear the little baby say her first word.

"One day, when Team Rocket is over and done with, Hope will be just like Ash, and she'll live her dreams and become a wonderful adult." He told Delia.

Delia gave him a small smile, appreciating his attempt to help.

"We'll get through this." Tracey continued. "Promise."


	4. Chapter 3

Latias flew through the night and part of the next day, carrying Ash halfway to Shamouti Island before stopping to rest.

"You did great, Latias." Ash told her. "Take a nice long rest." He was about to return her to her ball when he thought better of it. "I think it would be safer if I wasn't alone. I don't have Pikachu with me, so do you mind staying out her with me, Latias?"

Latias shook her head and lay against a tree. "La…"

Ash was about to lay down and go to sleep as well when he was hit from behind by a Shadow Ball.

"_Let Latias go!"_ A familiar psychic voice ordered.

Ash turned around just to get caught in a psychic attack. He tried to struggle, but could barely move.

"Mewtwo! Relax! I'm a friend!" He attempted. Mewtwo hit him with another Shadow Ball.

"_Why would a friend capture Latias?" _Mewtwo hissed.

"Arceus wanted me to! He sent me on a mission to protect the legendries! If I capture them, Team Rocket can't!" Ash cried.

"_Show your face!"_ Mewtwo ordered.

"I'm kind of being held still by _your_ psychic right now, meaning I kind of can't!" Ash retorted.

Mewtwo let him go and Ash took the hood and mask off.

"See, Mewtwo? I'm a friend." He said in his normal voice.

"_I did not realize it was you."_ Mewtwo replied. _"I thought you were one of them."_

"I guess that means the disguise works then." Ash said. "Sit down. I'll explain to you what's going on." His stomach grumbled. "But first, do you know where I can find some food?"

"_There is an abandoned Pokemon Center nearby. The food there is still fresh enough to eat. I'll show you the way."_ Mewtwo offered.

"Thanks, Mewtwo. I appreciate it. I need to put my hood back on in case someone sees us. Do you mind?" Ash said.

"_If that is what you wish to look like, I'm not going to stop you."_ Mewtwo said.

"Great." Ash put the hood and mask back on. "There'll be a nice bed there too. Come on, Latias."

They headed towards the Pokemon Center.

**Meanwhile…**

Tracey watched as Mrs. Ketchum and Hope slept. He could still hardly believe one of his best friends was dead. Not just that, but it had happened two years ago and nobody outside of the Team Rocket compound knew.

"But why?" He whispered. "Why did they kill him? It's not like he was the only one stopping them from taking over, right? He wasn't, so how many people other than Ash did they kill to get rid of their opponents?"

"They're still killing off opponents." Delia whispered.

Tracey started. "Oh! Mrs. Ketchum! I didn't realize you were awake!"

"Two thirds of the people who are arrested and taken to Team Rocket headquarters are killed within the first two days of being brought here." Delia continued. "Any long-lasting prisoners are killed only if they get sick."

"I guess you haven't gotten sick then." Tracey said, trying to ignore his worries of being part of those two thirds.

"I have." Delia replied. "But I'm Giovanni's 'play toy'. He won't kill me."

"I feel sorry for anyone who would have to be a criminal's play toy, especially if they're female." Tracey said.

"Yeah…" Delia said. "Get some rest, Tracey. You're probably going to face Giovanni in the morning."

Tracey shivered. "That's comforting."

"I know it's not, but you still need to sleep. If you appear sick…" Delia began.

"Okay, okay! I'll go to sleep!" Tracey interrupted, not wanting to hear the rest of that sentence. "Just… wake me up if anything happens."

Delia nodded. Both prisoners lay down, closed their eyes, and slowly drifted off to sleep.


	5. Chapter 4

Mewtwo was startled awake when he heard a door slam in the lobby.

Team Rocket agents marched into the Pokemon Center, led by Domino.

"Looks like we've found another legendary, although I don't know which one this is." Domino smirked. "Go! Entei!" She threw a Dark Ball.

Mewtwo growled as he fought against Entei. Domino called out Suicune and Raikou as well and he was soon outnumbered.

As soon as he was downed, Domino pulled out an empty Dark Ball. "Another one for the boss."

Before she could throw it, however, a Master Ball hit Mewtwo in the back of the head. Ash, who had gotten dressed and disguised quickly when he'd heard the battle raging downstairs, grabbed the Master Ball while it was still wiggling and fled out the door, calling out Latias and jumping onto her back as he ran.

Soon, they were off towards Shamouti Island again, leaving Domino and the grunts behind in angry shock.

**Later…**

Not far from Shamouti Island now, Ash willed Latias to land.

As soon as he touched the ground, he called Mewtwo out of his ball.

"Mewtwo, please forgive me! I was just trying to stop Team Rocket from capturing you! I can release you now if you'd like!" He said.

"_You were just trying to help, Ash, and this may be for the best. I was planning to follow you on your mission, anyway."_ Mewtwo said. Ash blinked in surprise. _"However, you need to promise me you will release me as soon as I ask, okay?"_

"Of course!" Ash replied. "Thank you, Mewtwo! I could use the help!"

"_Also, I'd like to be kept out of that filthy ball, understood?"_ Mewtwo added.

"No problem!" Ash said. "I would always keep Pikachu out of his pokeball too." He suddenly lowered his head at the thought of his best friend. "Pikachu… He must think I'm dead too…"

"_Maybe. Maybe not. Perhaps Pikachu still has hope that you are alive. A friendship like the one you share with Pikachu is not one easily broken."_ Mewtwo assured him. _"You'll be reunited with your pokemon eventually, but not now."_

Ash gave a small smile. "Thanks, Mewtwo. I appreciate it."

"_Let's get going then. We have work to do."_ Mewtwo smiled at the boy, who went to hop on Latias's back.

Then, they were back on their way to Shamouti Island, arriving about two hours later.

"Wow. This place looks like a ghost town." Ash mumbled. "I hope Team Rocket didn't get here first."

He directed Latias to Lightning Island, where Zapdos lived. Mewtwo followed close behind.

They landed on the Island and Ash called Latias back into her ball to rest.

"Let's find Zapdos." Ash said, starting off across the mountainous terrain.

It didn't take long to find Zapdos. The legendary attacked not long after sensing them on its island.

"_Zapdos, we mean no harm. Please, hear us out."_ Mewtwo said.

Zapdos glared at them, but seemed ready to listen. Ash explained his mission from Arceus and Giratina. Zapdos listened carefully before roaring in response.

"What did he say?" Ash asked Mewtwo.

"_He asked if you were planning to do this with Articuno and Moltres."_ Mewtwo translated.

"Oh. Yes. I'm planning to." Ash replied.

Zapdos looked at him suspiciously before asking, what Mewtwo translated to be, 'could I come and watch while you do it to them before letting you do it to me?'

Ash felt a little uncomfortable with this request, but agreed.

He soon found out Articuno and Moltres had similar ideas, so he had to capture them all at once.

"There." He said with a sigh of relief. "One more here and then we can move on."

"_Who dares capture Zaptos, Moltres, and Articuno?!"_ A voice shouted.

"I… I do!" Ash replied. "Because Arceus asked me too!"

"_Oh really…"_ Lugia appeared, flying up and landing on the ground in front of Ash and Mewtwo. _"Show your face!"_

Ash pulled off the hood and mask, quickly putting them back on when he heard voices and footsteps. "Quick, Lugia! Before Team Rocket gets here!"

"_Very well, Chosen One, but only for you would I do this."_ Lugia said.

The Master Ball had just dinged a successful capture when some Team Rocket agents rounded the corner of the volcano adorning Fire Island, led by Cassidy and Butch.

"Hey!" Cassidy shouted. "Who are you and where's Moltres?!"

They saw the Master Ball in Ash's hand and gasped.

"You filthy little dirt bag! You have no right to capture Moltres! You're not a part of Team Rocket! Who do you think you are?!" Butch yelled.

Ash thought quickly. "I am Shadow, and I'm going to be the one to take down Team Rocket once and for all. For now, I'll leave you be, but later, you will regret all you've done to the world."

He called out Latias, leaped onto her back, and left, headed for Sinnoh.

**Meanwhile…**

Tracey stumbled back into the cell he shared with Delia, who was relieved to see him.

Giovanni hadn't ordered him killed. Instead, he was to be kept alive and tortured.

When he told Delia what they were planning to do with him, she was appalled.

Quickly searching for a bright side, she said. "At least they're not going to kill you. Hopefully, you'll still be alive at the end of all this."

"It's highly unlikely." Tracey mumbled. "And torture isn't much better than death."

"Don't think that way, Tracey! You need to look at the bright side of things!" Delia exclaimed.

Tracey sighed and thought about the good old days. The days before the war started. The days his only worries were whether or not the pokemon were fed on time and whether or not the Professor got done everything he needed to. The days when Ash was still alive and they were stopping Team Rocket at almost every turn. The days when nearly everyone was happy.

How he wished those days would come back! However, deep down, he knew that would never happen. With Ash gone, things would never be the same ever again.

That night he dreamed of a person riding on a Latias with an unknown pokemon flying beside them. It was dark out and the three landed somewhere Tracey didn't recognize. Tracey dreamed of a pokemon he recognized as a Darkrai. The person spoke to the Darkrai, but Tracey couldn't make out the words. Then, the person held out a Master Ball and the Darkrai willingly went inside.

Team Rocket rounded the corner and the person said something before fleeing on Latias.

This time, Tracey heard the words. "I am Shadow and I'm going to be the one to permanently take down Team Rocket. For now, I leave you be, but later, you will regret all you've done to the world."

Team Rocket chased him on Staraptors and Pidgeots, but the person got away easily with Latias's speed, the unknown pokemon keeping up pace.

That was when Tracey woke up.

Some Team Rocket grunts were in the cell, whipping him in order to wake him up.

Tracey winced and whispered. "Okay. I'm awake."

The grunts grunted in satisfaction and pulled him to his feet. They took him to a torture chamber and… well… tortured him.

By the time he was led back to his cell, Tracey was covered in bruises.

Since it was the middle of the night, He managed to quickly fall back asleep, all the while wondering about his dream.


	6. Chapter 5

Ash smiled as he looked at the Master Ball holding Darkrai. It had been rather easy to capture him. Darkrai had already been afraid Team Rocket would hurt him and, upon recognizing Ash and receiving an explanation, was very willing to join up.

"_Where are we headed now, Shadow?_" Mewtwo asked.

"Unova." Ash answered. "And thanks for agreeing to call me that. It will really help us if we run into anyone I know."

"_There were no more legendries in Sinnoh?"_ Mewtwo wondered.

"Most of them have been captured and Dialga and Palkia are hidden well enough that I probably don't have to worry about them." Ash replied. "But there are a whole bunch of legendries in Unova that need protecting."

"Where in Unova are we going first?" Mewtwo asked.

"An area once known as the Kingdom of the Vale." Ash answered. "I'm hoping Victini has returned there in hopes of finding safety. It might take a few days to fly there, though. Unova is far away from here, even if you and Latias are fast."

Mewtwo nodded. _"I understand."_

**Two weeks later…**

Ash ripped a wanted poster of himself and Mewtwo off a wall in Eindoak Town and tore it to shreds.

He turned to Mewtwo. "This is the place. Let's just hope we're not found."

"_Even if we are, they're not going to be able to capture us."_ Mewtwo pointed out.

"You're right. I'm worrying for nothing." Ash agreed. "Now let's find Victini."

"Tini!" Victini flew up to them and landed on Ash's shoulder.

"_That was easy."_ Mewtwo commented as Ash explained to Victini what was going on.

"Tini?" Victini looked uncomfortable.

"There he is!" Ash and Mewtwo spun around to see Team Rocket, led this time by Jessie, James, and Meowth, running towards them.

"That must be Shadow!" James said.

"Don't let him take Victini! We need him for the boss!" Jessie ordered.

Ash turned back to Victini and pulled out a Master Ball. "Victini, it's me or them."

Jessie whipped out a Dark Ball and threw it towards Victini.

Victini panicked. Ash quickly pushed the legendary out of the Dark Ball's path. Jessie growled in frustration.

"Victini! Choose!" Ash yelled.

"He don't have a choice!" Meowth shouted. "He's coming with us!"

Victini pressed the button on the Master Ball, which only wiggled a few times before signaling a successful capture.

Ash pushed Victini's ball in his bag before leaping onto Latias's back and fleeing. Mewtwo followed.

**Meanwhile…**

Tracey woke up from yet another dream about Shadow. This time, Shadow had captured Victini, his first capture since Darkrai. The rest of the dreams were relatively unimportant, but Tracey was really curious. He longed to see Shadow's face and find out who he was and why he was after legendary pokemon. He obviously wasn't a part of Team Rocket since, in his dream, Shadow had torn down a wanted picture of himself, so why was he after legendary pokemon?

Was he planning to fight a battle against Giovanni?

"Whoever this Shadow guy is, Giovanni sure is pissed at him." Tracey heard a grunt saying from outside his cell.

He stifled a gasp. Shadow was real? That meant these weren't just dreams! They were happening in the world right now!

'If Team Rocket finds out, they'll force me to reveal his location.' Tracey thought to himself. 'I've got to keep quiet about my dreams or I'll be in more trouble than I already am.'

The door opened and Tracey pushed himself up, knowing it was time to be tortured.

To his surprise, they took Delia instead, but not before she could push Hope into Tracey's arms.

Delia didn't return that night or the next day. Not even the day after that did she return.

And Tracey knew what had happened to her.


	7. Chapter 6

"Zekrom will be hard to find." Ash said. "I have no idea where to look for them."

"_Hopefully, he will come to us like Victini did."_ Mewtwo replied.

"Maybe we can find the legendary musketeers easier. We'll save Zekrom for later." Ash decided.

"_You know where to find them?"_ Mewtwo asked.

"I think so." Ash responded. "Come on. Let's go."

They soon arrived in the place where Keldeo, Cobalion, Virizion, and Terrakion lived.

Keldeo was willing to join as soon as Ash showed his face. Cobalion, Virizion, and Terrakion were a little more reluctant, but soon agreed as well.

Ash had just completed the captures and put his hood and mask back on when not Team Rocket but Iris and Cilan rounded the corner! The two were leading a group of trainers that Ash figured were rebels, part of the Resistance.

"Release the legendries at once!" Iris ordered of him.

Ash didn't know what to say to his friends, so Mewtwo answered for him. _"What we're up to is none of your business, girl!"_

Iris frowned. "What kind of pokemon are you?"

"_That is also none of your business, girl! Now leave us be!"_ Mewtwo growled.

"No way!" Iris replied. "You're coming with us!"

"_Over my dead body!"_ Mewtwo nearly shouted.

To Ash's and Mewtwo's surprise, Iris pulled out a gun and pointed it at Ash, who froze. "I don't want to use this, but I will if I have to. Again, release the legendries."

Ash hesitated for a moment. "No!"

"I think I misheard you. What did you just say?" Iris said.

"I said 'no'. I won't release the legendries at the moment." Ash spoke slowly, careful with his words. "And if you shoot me, I assure you that you will regret it."

Iris growled at him and started to pull the trigger.

"Iris, no." Cilan said. "Save the tranquilizer darts for another time. Let's try to reason with him."

"What makes you think he'll listen to us?!" A female rebel called.

"I've seen wanted posters of him all over. Team Rocket's after him, which means he's not one of them." Cilan said.

"But he's not one of us either, so whose side is he on?" A male rebel asked.

"Yeah! Whose side are you…" Iris began, turning to see… no one. "Hey! He's gone!"

"Let's inform the rest of the Resistance about him." Another female said. "He could be one of them and the posters are just to throw us off. It's best to be careful. After all, he does have legendary pokemon with him."

"Good point." Iris said. "Let's just hope that guy is on our side."

**Later…**

Ash passed a mirror absentmindedly, before quickly doubling back as Giratina appeared.

"What is it, Giratina?" Ash asked the legendary. Mewtwo came up behind him.

"_I came to update you. Zekrom and Kyurem have been captured by Team Rocket. Also, I have not seen Arceus since a few days before you woke up. I fear he might have been captured as well, but Team Rocket has seen no signs of having him."_ Giratina told him.

"They might have Arceus?" Ash asked fearfully.

"_I'm afraid so."_ Giratina replied. _"Tell me, how is your progress?"_

"With the exception of Palkia, Dialga, Celebi and you, I've captured all of the free legendries I know of." Ash responded. "I figured I shouldn't bother Palkia and Dialga since they are in their own realms and I don't think Celebi is in this time period right now."

"_As long as they stay in their own realms, they will be safe."_ Giratina agreed.

Suddenly, a red light enveloped Giratina and he shrank into a ball, revealing Domino and several rockets standing behind him. Domino was holding a Dark Ball.

"NO!" Ash cried.

"How does it feel to have one taken right out from under you, Shadow?" Domino teased.

"You're going to pay for this!" Ash yelled.

Domino whipped out a gun. "You're going to pay first!"

Mewtwo tried to put up a barrier, but wasn't fast enough to block it from hitting Ash. Ash blocked the bullet from causing a fatal injury with his arms.

He grabbed his lower right arm after the bullet hit and fell to his knees, cringing in pain. Mewtwo's barrier stopped any more shots from hitting them.

Domino's gun finally ran out of bullets and she grabbed another one, continuing until all the guns the group had brought with them had run out of bullets.

Seeing his chance, Mewtwo grabbed the now-fainted Ash and flew away as fast as he could. Knowing Team Rocket would give chase, he hastily poured on the speed, landing in Nacrene City as soon as he got away.

"_Shadow. You must wake up."_ He urged, gently shaking the boy. _"You are hurt. Sleeping is not an option."_

Looking around, he ran to the abandoned Pokemon Center and searched for bandages. Soon, he had cleaned and bandages the injury, but Ash had still lost a lot of blood and was very pale.

"_What do I do now?"_ Mewtwo wondered.

The door to the room they were in slammed open, revealing Lenora, the ex-gym leader of Nacrene City.

Mewtwo turned to face her. _"What do you want? Can't you see I'm busy?"_

"Out of my way!" Lenora yelled.

Mewtwo, who had taken off Ash's cloak and mask in order to treat him, refused to move. _"You will not touch Shadow!"_

"So Shadow's his name, huh? We've been warned about you. From what I've heard, you're not on our side. So get out!" Lenora ordered.

Ash stirred behind Mewtwo. Opening his eyes, he saw Lenora and realized his disguise was off. Fortunately, Lenora seemed too preoccupied with Mewtwo to notice.

Carefully, Ash slid off the table Mewtwo had placed him on and snuck over to get his cloak. Unfortunately, he didn't make it that far and collapsed halfway there.

Both Mewtwo and Lenora heard the thump when Ash hit the ground and turned to see him fully revealed.

Lenora gasped while Mewtwo rushed to his side.

"_Shadow. Shadow, wake up."_ Once again, Ash was unresponsive.

"It can't be…" Lenora whispered. "He disappeared years ago… Before the war started…"

"Mew… Mewtwo…" Ash mumbled.

Lenora noticed the bandage on Ash's arm. "What happened to him?"

"_That is none of your concern, woman!"_ Mewtwo snapped.

"I can help! I know medical treatment!" Lenora replied.

Mewtwo hesitated.

"Look." Lenora said. "I know I was hostile before, but the Resistance is using this as a hideaway. I'm on guard duty right now. I know that Ash isn't the type to betray us. I doubt you two mean any harm."

Mewtwo tensed. _"You are not to tell anyone Ash is alive. Do you understand? It is important Team Rocket doesn't find out that he survived when they supposedly killed him over two years ago. Call him Shadow and tell no one he is Ash."_

Lenora nodded. "I understand, but please let me help! He needs treatment right now!"

"_I guess that if Ash is a friend of yours, I'm forced to trust you as well. Harm one hair on his head and you'll regret it."_ Mewtwo finally agreed.

They gently laid Ash back on the table and Lenora used the Pokemon Center supplies to treat him.

"He needs rest now." Lenora said when she was finished.

"_And we must move on. Help me put the cloak and mask back on him."_ Mewtwo said.

"I'll help with the cloak, but it's better if we don't put the mask back on him. He will breathe easier without the mask." Lenora suggested.

Mewtwo agreed reluctantly, putting the mask in Ash's bag. Soon, Ash was ready for travel, as in being carried through the sky by Mewtwo.

"Be careful with his arm. It's badly broken." Lenora instructed as Mewtwo put Ash's bag over his shoulder and picked up the boy. "Take care of him and replace his bandage at least once a day." She put some bandages in Ash's bag. "Be careful out there."

"_We will be."_ Mewtwo replied before leaving the building and taking off into the night.

**Meanwhile…**

Tracey fed Hope with some baby food Team Rocket had been kind enough to provide. He wished Delia was still there. Hope had been crying a lot since her mother had left her.

Tracey thought back to his last dream about Shadow. Shadow had been hurt by a Team Rocket agent Tracey had never met and the pokemon that accompanied him had managed to get him out of there. They had met up with Lenora, whom Tracey knew was a gym leader in Unova. That meant Shadow was somewhere in Unova right now and he was extremely vulnerable at the moment. Lenora seemed to recognize Shadow, although, at that point in the dream, Shadow was just a silhouette to Tracey.

"Who are you, Shadow?" Tracey whispered under his breath. "Why are you invading my dreams?"


	8. Chapter 7

**Three weeks later…**

"_Are you sure this is the best course of action, Shadow?"_ Mewtwo asked. _"You still have a broken arm."_

"We've already captured all of the legendary pokemon I know of that were still roaming free." Ash pointed out. "I wasn't told what to do next, so I'm choosing for myself. The legendries Team Rocket has need to be rescued. Once I've rescued them, I'll come up with a plan to defeat Giovanni. I won't let my arm get in the way of that."

"_I see…"_ Mewtwo said. _"So what's the plan?"_

"We sneak in through the roof and find out where they're keeping the legendries. After that, we're going to have to improvise." Ash replied. He called Latias out. "Latias, we need to get to the roof. Also, we can't be seen."

"La!" Latias agreed and Ash climbed onto her back. Latias flew him up to the roof. Then, Ash put her back into her ball and started looking for a way in. As far as he knew, nobody knew he was there.

**Meanwhile…**

Tracey woke with a start. Shadow was there. He had to find a way to get Shadow to rescue him and Hope and fast.

The door to the cell flew open. Tracey barely had the chance to pick up Hope before he was being dragged and shoved down the halls.

"Say your goodbyes to that baby, boy. She's going to be raised by Team Rocket." One of the Team Rocket agents sneered.

Tracey glared at him. "I'm not letting you take Hope!"

"You have no choice, boy! The boss has ordered you killed!" Another Team Rocket agent snickered.

The words echoed in his head. He was going to be killed. Unless…

"You won't win!" Tracey shouted. "I have friends in high places!"

"Oh yeah? What kind of friends?" The first rocket questioned.

Tracey didn't answer.

"We knew you were bluffing." The second rocket laughed. "Just be glad you're not being executed alone. We have some others being killed today as well."

As they emerged into the execution room, which Tracey had never seen before, the boy saw some other prisoners cowering in a corner, surrounded by guards with whips.

The execution room had corpses lining the walls. Tracey spotted Delia's corpse among them. Hope started crying, reaching for her mother. Tracey held the baby tight as he was led over to the other prisoners.

Giovanni strolled into the room shortly after, the corpses not disturbing him even the tiniest bit.

"Now, which one of you wants to go first?" The Team Rocket Boss sneered.

Everyone but Tracey took a step back.

Tracey gulped. He could only pray that Shadow got there in time.


	9. Chapter 8

Ash snuck through the halls quietly, Mewtwo walking beside him.

Suddenly, Mewtwo stopped while Ash kept walking. _"Shadow! In here!"_

Ash backed up and looked inside the room. He grinned when he saw a bunch of Dark Balls being guarded by a couple of Team Rocket grunts who weren't looking in their direction.

Ash whispered a plan into Mewtwo's ear before slipping out of sight.

Mewtwo threw a Shadow Ball at the grunts, grabbing their attention.

"Hey!" Grunt #1 shouted. "Get out of here!"

"Actually, don't bother leaving! We'll just capture you!" Grunt #2 yelled with a wild grin.

He pulled out a Dark Ball and threw it, revealing an Absol.

"Sol!" Absol roared.

Behind the grunts, Ash shivered before grabbing all of the Dark Balls on the table and slipping out of sight once more.

"Sol?" Absol looked around.

"Absol, use Night Slash!" Grunt #2 yelled.

Absol used the move, but not on Mewtwo. Mewtwo gasped as Ash was hit, his wound reopened. The boy hit the ground hard as the grunts stared at him in shock and anger.

"That's the boy everyone's been talking about! Shadow!" Grunt #1 shouted. Both grunts spun around to see that the Dark Balls were gone. "He's got the legendries! Get him!"

Mewtwo scooped up Ash and raced out of the room. Grunt #2 hit the alarm, which blared throughout the building.

**Meanwhile…**

Tracey breathed a sigh of relief as the alarm distracted Giovanni and the Team Rocket grunts, allowing him to slip away unnoticed. He still held Hope in his arms. Giovanni had been about to kill both him and the baby.

The other prisoners had managed to slip away as well, but the cry of outrage in the room behind them showed they wouldn't be missed for long.

"RUN!" Tracey yelled, taking the lead.

The group ran through the halls, dodging Team Rocket grunts who tried to stop them at every turn and grabbing their pokemon on the way out.

Eventually, they reached fresh air, but they weren't out of the woods yet. Running into Viridian Forest, they didn't lose them until they were halfway to Pewter City.

"Is everyone here?" Tracey asked, looking back at the group.

Everyone looked around at each other before confirming that no one was missing.

"Good." Tracey said. "Let's hike off the path a bit and find a place to set up camp. I'll make us something to eat."

"Who made _you_ leader?!" An older girl exclaimed. "You're just a kid! With a baby!"

Tracey glanced at Hope. "So? At least I'm doing _something_."

Everyone else shifted uncomfortably.

"Now, let's get out of sight so that Team Rocket doesn't manage to catch up to us." Tracey said. "Come on."

**Meanwhile…**

Mewtwo laid an unconscious Ash down not far from where Tracey and co. were setting up camp.

The boy was very pale, having lost a lot of blood over the past couple of hours.

"_He needs a type of help I can't give..."_ Mewtwo murmured absentmindedly. _"But where can I take him? Team Rocket is surely searching for him. Who is able to help us?"_ Just then, Brock and Misty's faces came to mind. _"His friends. Where can I find them? They will surely be fighting with the Resistance, but where can I find the Kanto Resistance?"_

Just then, he heard footsteps. Someone was coming.

**Meanwhile…**

Tracey and co. looked up when they heard footsteps.

Tracey quickly grabbed a rock and threw it in the direction the sound was coming from. The rest of the group followed his example.

"Woah! It's okay! We're not with Team Rocket!" Another group, wearing ski masks, stumbled into the clearing.

Tracey's group temporarily halted their throwing.

"Who are you?" One of the escapees asked.

"They're part of the Resistance." Tracey said. "Am I right?"

"Tracey!" Misty pushed her way out of the group, yanking off her ski mask and racing over to hug Tracey.

"Misty!" Tracey replied in both surprise and happiness.

"Tracey! I thought I'd lost you!" Misty said, crying with joy.

Tracey smiled. "I thought I was going to die, but we managed to get away."

Hope crawled over and tugged on Tracey's pant leg with her little hands. Tracey picked her up.

"Whose baby is that?" Misty asked, surprised.

"It's Mrs. Ketchum's baby. Her name is Hope." Tracey answered, wincing.

Misty looked around. "Where's…"

"She's dead. They killed her." Tracey answered quickly.

"That must mean… Hope's an orphan… and so is Ash…" Misty murmured.

"Misty…" Tracey began. He didn't get to finish the sentence.

"Well, there's an underground passage leading to base not far from here." One of the other rebels interrupted. She turned to her fellow Resistance members. "Check them for trackers. Then, we'll leave the guard duty to Brock's group. I'll contact him to let him know."

**Meanwhile…**

Mewtwo guarded Ash carefully against the group of ski-mask-wearing people.

One of the people took off their ski mask. "Mewtwo?" It was Brock.

Mewtwo blinked in surprise before glancing at the rest of the group uneasily.

Brock glanced at them too. "They're not going to hurt you. We can all help you."

Mewtwo looked behind him at Ash's pale face. The boy was getting worse, giving Mewtwo no choice.

The pokemon put the mask back on Ash's face and picked him up gently.

"_Normally, I would not trust so easily, but he needs help badly. Waiting is not an option."_ He said.

Brock nodded in understanding. "Let me see him. I was studying to be a doctor before the war. Perhaps I can help." He pulled a first aid kit out of his bag as Mewtwo laid Ash onto the ground once more.

Brock gently pulled up Ash's sleeve revealing the reopened wound. Mewtwo hadn't had any bandages left to recover it after the old bandage had fallen off thanks to the Absol.

Brock gently cleaned the wound, resulting in some flinching and wincing from the unconscious boy. Then, Brock stitched up the wound carefully before wrapping it in bandages. After that, he fashioned a sling out of some leftover bandages and stood up to admire his work.

"_Thank you."_ Mewtwo said, picking up Ash. _"We must be going now."_

"He needs blood." Brock announced before they could leave. "You need to come back with us to base."

Mewtwo turned back to face him. _"Pardon?"_

"His skin is too pale. He's lost too much blood. If we don't get him some more soon, he might die." Brock explained.

Mewtwo thought it over. _"Fine, but you'd better not have ulterior motives for this."_

"I promise that we don't." Brock assured him. "Now let's hurry."

**Meanwhile…**

Tracey and co. followed Misty and co. to the secret entrance. Brock and co. were already there, Mewtwo carrying Shadow not far behind.

Tracey glanced at Mewtwo and Shadow, knowing they had probably been the ones who had set off the alarm that had allowed his, and the other prisoners', escape.

"Brock, what's wrong with that boy?" He dared to ask.

"He's injured. He's lost too much blood. He needs help." Brock answered before realizing who he was talking to. "Tracey! I barely noticed! Thank goodness you're okay!"

Tracey gave a small smile but was too worried about Shadow to answer.

"Um, Mewtwo, what's his name, anyways?" Brock continued.

"_He is going by the name Shadow."_ Mewtwo answered.

"I see… That sounds more like a codename than a real name." Brock said. "Is that his real name?"

"_It is what he would like you to call him for now."_ Mewtwo replied.

"Uh… okay then…" Brock murmured. "Misty, some of us need to stay out here and keep guard. We can't leave the place unguarded."

"I agree." Misty said. "You need to go because you're a doctor. Half of my group and half of your group will stay behind. I'll stay with them."

Brock agreed to the plan and they split up, said their goodbyes, and half set off for base while the other half stood guard.

**(A/n) Ash will be called Shadow in Tracey's accounts until he knows who Shadow actually is. Hope you are enjoying the story so far. (A/n)**


	10. Chapter 9

Mewtwo watched as Brock withdrew some blood from Ash's arm. _"You said he needed blood, so why are you taking some from him?"_

"I need to know his blood type and he can't exactly tell me when he's unconscious." Brock said. "It'll only take me a few minutes to figure it out. Then, we can find someone willing to donate some blood to him." With that said, Brock left the room, leaving Mewtwo and Ash alone, but not for long.

"Um… hello." Tracey said, walking nervously into the room. "I… Is he going to be okay?"

"_I hope so."_ Mewtwo responded. _"Who are you, anyways?"_

"My name's Tracey. I'm Professor Oak's assistant. At least, I was…" Tracey trailed off. "You were the ones who set off the alarm in the Team Rocket base, weren't you?"

"_Yes… how did you know that?"_ Mewtwo asked.

"Thank you. They were about to kill me and Mrs. Ketchum's baby, Hope. You probably don't know who Mrs. Ketchum is, but… it doesn't matter if you know her or not. They killed her, just like they did so many others. I… I still cry about it sometimes. She was such a nice woman. They killed her son too. He was one of my best friends. I'm going to raise Hope for them, since they can't." Tracey paused. "I'm rambling, aren't I? Sorry. I just wanted to say that if you hadn't set off that alarm, Hope and I, and all the other prisoners that were set to be executed at that time, would have never escaped. Thank you."

He stood up as Brock came back in. The older boy didn't question his presence there. He just asked. "Are you a blood type A?"

"Uh… yeah? Why?" Tracey asked, confused.

"Shadow really needs a blood donation or he'll die. He's a blood type A." Brock explained. "Do you think you could…"

"Sure!" Tracey agreed. "But you'd better agree to help me keep an eye on Hope if I'm weak afterwards! You know how energetic babies can be!"

"Okay. Deal. Where'd that baby come from, anyways? Some woman you were sharing a cell with who Team Rocket killed?" Brock asked.

"Right on the dot." Tracey replied, wincing. "Come on. Let's get this over with."

"Right!" Brock agreed, snapping back to the present.

He transferred some blood from Tracey to Ash, and soon Ash's skin color was just about back to normal.

"Thanks, Tracey. Why don't you go back to your new room for some rest?" Brock suggested.

Tracey slipped off the table he'd been laying on during the transfer and stumbled a bit. "Okay." He nearly fell, but Brock caught him.

"I'm going to help Tracey get to his room." Brock told Mewtwo. "I'll be back."

"_Alright. Thank you."_ Mewtwo said. As soon as Brock and Tracey had left the room, the pokemon put Ash's bag over his shoulder, picked up the injured boy, and was gone by the time Brock came back.

Brock sighed. "At least Shadow will be able to get better now."

He turned and left the room again.

**Meanwhile…**

Tracey played with Hope a little bit, making the baby giggle and gurgle, but he was back in bed when Brock came to check on him.

"Hey, Brock. What's up?" He asked. "Wait! Hope!"

Brock looked down to see the 14-month-old baby crawling out of the room, just past his feet.

He scooped her up and deposited her on Tracey's lap before sitting down at the foot of the bed.

"Mewtwo and Shadow were gone when I returned to the room. Mewtwo only trusted us long enough for us to give treatment to Shadow, then, he took Shadow and left." He said. "It was a good thing we did all we needed to do for him. It's also a good thing he took the bandages from my first aid kit as well."

Tracey nodded in agreement. "I'm just glad I was able to help."

"I wonder why they left so quickly and why Mewtwo wouldn't let us see what was in the bag." Brock added.

Already knowing what was in the bag, Tracey just shrugged and said. "Maybe they just didn't want us thinking wrong of them."

"They must be on our side, though. Otherwise, there wouldn't be wanted posters of them hanging up all over the world." Brock said.

"They're on wanted posters?" Tracey asked, trying to act surprised.

"Yes. I didn't really see the posters though. I just heard about them." Brock replied.

"I'll be on wanted posters before you know it." Tracey murmured, hanging his head.

"No biggie. The people on wanted posters are hailed as heroes these days. Anyone brave enough to end up on a wanted poster is brave enough to be a hero." Brock said with a smile.

"That was more of Ash's thing." Tracey murmured.

"What do you mean 'was'?" Brock asked.

"Brock, Ash is dead. They killed him over two years ago." Tracey said quietly. "They tortured his mother. That's where Hope came from. Then, they killed his mother as well."

Brock stared off into space, hardly able to register what he'd just been told. "Are you sure he didn't… escape? Like you did?"

"If he'd escaped, we would've known by now." Tracey mumbled.

Brock was silent, not knowing what else to say.

"Can we stop talking about this now? Please?" Tracey asked. "I… I miss them…"

"I miss them too, Tracey, and that's not going to change. Now, you should relax and think happy thoughts. There's a meeting in a few minutes I have to go to. Stay here." Brock said. He got up and left.

"A meeting, huh? Wonder what it's about." Tracey murmured.


	11. Chapter 10

Mewtwo laid Ash down gently on his bed in Pallet Town. The house had been abandoned for years and it was the last place someone would think to look for them.

The boy hadn't woken up since not long after the Night Slash had hit him, and it didn't look like he'd be waking up anytime soon either.

"_I wish we had a Celebi to help us out."_ Mewtwo said to himself. _"Shadow would recover much quicker that way, but Celebis only appear in times of peace, so it would take more time to find one than to just let him heal naturally."_

"Mewtwo…" Ash moaned.

Mewtwo blinked. It seemed he had overestimated Ash's injuries.

The boy struggled to open his eyes. "I feel weak."

Mewtwo felt Ash's forehead, as he had seen humans do when trying to figure out if another human was sick. It felt warm.

"_You might have a fever."_ He told the boy.

"Great. Just great." Ash said sarcastically. "Could the situation get any worse?"

"Check that house! It's been abandoned for years so they might take refuge in there!" They heard someone shout.

"Apparently, it can." Ash mumbled.

Mewtwo picked up Ash's bag again before scooping up the boy.

He opened the window and flew out into the night.

There was some shouting from the ground and the sound of pokeballs opening.

"They're chasing us…" Ash whispered.

"_We'll get away."_ Mewtwo promised.

A Gust attack hit Mewtwo, causing him to almost drop Ash. He tightened his grip on the boy so that nothing would happen to him.

"Don't drop me, Mewtwo…" Ash murmured.

"_Don't worry. I won't."_ Mewtwo said.

The chase went on for a few hours before Mewtwo and Ash finally lost their pursuers.

They were in Johto now, in the forest near Arborville.

Mewtwo placed Ash down in front of Celebi's shrine and looked around.

"_We'll be safe here for now."_ He said.

Ash nodded slowly, still unable to open his eyes.

"Bi! Lebi!" Mewtwo spun around at the noise. "Bi! Lebi!" A Celebi flew up to them.

"Is… is that Celebi?" Ash asked.

Mewtwo nodded before remembering the boy couldn't see him. _"Celebi, can you help us? Shadow is unable to open his eyes. He is sick."_

"Bi!" Celebi gave a quick nod and flew away. It came back with some berries and used some of its magic to heal Ash's arm.

Mewtwo fed Ash the berries and soon the boy was able to open his eyes and sit up.

"Thank you, Celebi. Thank you, Mewtwo." He said quietly.

There was a shout from far away that sounded strangely like "I think it went this way!"

Ash explained his mission to protect the legendries to Celebi. Being the Celebi that had helped save Ash's life the night he would have died, it already knew and agreed quickly.

Ash caught it in a Master Ball and got to his feet wobbly, picking up his bag as he went. Mewtwo caught him before he fell down.

Just then, some Team Rocket agents burst into the clearing.

"Where's Celebi?" They shouted.

Mewtwo scooped up Ash once more and flew away before the agents knew what had hit them.

"Where are we going now, Mewtwo?" Ash asked.

"_Somewhere where we can release the pokemon in the Dark Balls without anyone seeing_." Mewtwo answered. _"The place where I was made."_

Ash nodded and fell asleep in Mewtwo's arms. The clone woke him up when they got to New Island.

"_Here is a safe place."_ He said.

Ash nodded and got out the Dark Balls. He released the pokemon inside one at a time, taking the time to explain the situation to each one of them and recapture them in Master Balls.

When he was done, he turned to Mewtwo. "We're still missing Giratina, Entei, Suicune, Raikou, and Arceus."

"_You're going to capture Arceus?"_ Mewtwo questioned.

"Only if I have to. The point is that Team Rocket still has them, and that means trouble. I don't know if all the legendries in the world could stand up to Arceus." Ash said. "And they can get into the Reverse World and mess up the Real World a lot with Giratina. Not to mention, those two are the ones who gave me the mission in the first place."

Meloetta popped out of her ball and landed on Ash's shoulder. "Letta!"

"Hi, Meloetta. I'm sorry I didn't get to you before you had to go through all that with Team Rocket." The boy said.

"Letta!" Meloetta nodded happily in forgiveness.

Ash broke the empty Dark Balls and threw them into the ocean. "That takes care of that. Let's stay here for a while, Mewtwo. We're safe here."

"_Alright, Shadow. We can train here before going up against Giovanni."_ Mewtwo agreed.

Ash frowned and looked out at the ocean. "Do you really think I can beat him, Mewtwo? He has Arceus and Giratina on his side, after all."

"_If it makes you feel better, the rebellion can come with us."_ Mewtwo said.

Ash shook his head. "There could be double-agents and double-agents might let Giovanni know we're coming. I don't want him to have any warning."

"_You are right, but you won't be alone. All of the legendries you have with you will be going too." _Mewtwo reminded him.

Ash nodded. "Yeah. You're right. I'll have plenty of help, and, when it comes time to battle, I'll have plenty of support too. Everyone's counting on me, so let's start training!"

**(a/n) It's a little rushed, sorry, but I did my best. (a/n)**


	12. Chapter 11

Weeks passed as Ash worked with the legendary pokemon.

He had to work hard to remember all their moves and help them get ready to face Arceus and Giratina.

Finally, he decided they were ready. With perfect timing too, because the day he decided they were ready was the day Giovanni found out where they were.

The evil Team Rocket leader arrived on the island just as Ash had put the last of the legendary pokemon (excluding Mewtwo) in his bag and was putting on his mask.

"So… You're the infamous Shadow…" Giovanni sneered, causing Ash to spin around in surprise.

Mewtwo growled in anger. _"And you're the evil creep who thinks he can rule the world._"

Giovanni ignored the clone. "I challenge you to a battle, Shadow. If you lose, you hand over every legendary pokemon you have on you."

Ash hesitated. "And if I win?"

"Simple. You won't." Giovanni smirked.

"No deal." Ash said. Several Team Rocket agents surrounded him.

"I don't believe I was giving you a choice in the matter, Shadow." Giovanni growled. "Either you battle to keep them, or you hand them over right now."

"If I win, you're going to surrender yourself and give me all the legendries in your organization." Ash commanded slowly.

Giovanni frowned. "Since you're not going to win, I guess it won't hurt. Alright, deal." He held out his hand and Ash cautiously shook it.

They went to opposite sides of the makeshift battlefield Ash had been using for training.

"The rules are all the legendries you have against all the legendries I have." Giovanni announced.

"Darkrai! I need your help!" Ash called, throwing Darkrai's master ball. Darkrai appeared on the field.

"Arceus, show him your power." Giovanni threw a dark ball, releasing Arceus.

Ash flinched, but did his best not to show that he was nervous.

"You may have the first move." Giovanni said.

"Use Hypnosis! Then, use Nightmare!" Ash called.

"Arceus, dodge and use ExtremeSpeed!" Giovanni countered.

"Dodge it!" Ash said, but wasn't quick enough. Darkrai was hit by ExtremeSpeed. Ash bit his lip. "Try Hypnosis again!"

"Don't let them land an attack! Use Punishment!" Giovanni ordered.

"Double Team!" Ash said. Darkrai multiplied and Arceus didn't know where to land the attack. "Hypnosis!"

"Dodge it!" Giovanni ordered, but Arceus didn't know where the attack was coming from and failed to dodge.

"Use Nightmare and then Dream Eater!" Ash ordered. The attacks scored direct hits and caused a lot of damage. "Now use…"

"Arceus, use Hyper Beam!" Giovanni interrupted. The attack knocked Darkrai out immediately. Giovanni grinned. "Send out your next pokemon."

Ash cursed under his breath, returned Darkrai, and sent out Celebi. "Celebi! Use Heal Block!"

Celebi obeyed, successfully blocking Arceus's healing abilities.

"Now use Leaf Storm!" Ash continued.

"Counter with Judgement!" Giovanni called.

Arceus didn't move and was hit by the Leaf Storm.

"You forget that a pokemon can't move for a bit after using Hyper Beam!" Ash yelled, grinning. "Celebi! Use Perish Song!"

"Arceus, dodge it!" Giovanni screamed.

Arceus attempted to dodge it, but was hit with the attack anyways. Ash grinned. The battle was going his way.

The grin was wiped off his face when Celebi was knocked out when Arceus used Hyper Beam again.

He scowled and returned Celebi, reminding himself it wasn't over till it was over.

He summoned Meloetta, who quickly changed into her Pirouette Form and used Close Combat, which proved to be the final straw to knock Arceus out.

"Great job, Meloetta!" Ash called.

Giovanni growled and returned Arceus. "You won't be cheering for long, boy. Let's see how you deal with your old friend, Giratina!"

He released Giratina onto the battlefield.

"Meloetta, return!" Ash called. "Rayquaza! I need your help!"

And the battle continued.

**(A/n) I know. Lame battle scene. I'm not very good at battle scenes, but at least I updated! (A/N)**


	13. Chapter 12

The battle, Shadow versus Giovanni, was long underway when the rebels arrived riding their pokemon.

"What's going on over there?" Iris whispered.

They had long been using the abandoned island as a meeting place for different rebel groups, but there seemed to be a battle going on that worried the rebels.

The rebels snuck through the ruins to get a closer viewpoint. They were surprised to see the legendary battle raging on the makeshift battlefield that hadn't been there last time.

Iris and Cilan's group saw Misty and Brock's group on the other side of the battlefield. They waved to signal they were there. Misty and Brock's group waved back.

"Rayquaza, use Dragon Claw!" Shadow yelled.

"Giratina, Dodge it!" Giovanni responded.

"Keep using Dragon Claw until it hits!"

"Use Shadow Claw!"

The battle went on with the pokemon using attacks and missing each other until both were tired out and were knocked out at once.

"Great job, Rayquaza."

"Is that the best you've got, Giratina? Entei! Show me your power!"

"Regirock, I'm counting on you!"

Giovanni gritted his teeth. Shadow had the type advantage, but he couldn't substitute just because of that. "Entei! Fire Blast!"

"Dodge and use Stone Edge!" Shadow countered.

Giovanni growled as the Fire Blast missed and the Stone Edge hit. "Use Fire Blast again! Melt that piece of rock!"

This time the Fire Blast hit and Regirock got a burn as a side effect.

"Regirock! Keep going! Use Hyper Beam!" Shadow called.

"Risky move. You said yourself the pokemon has to rest after using the move. Entei, dodge!" Unfortunately, Giovanni told Entei too late to dodge and he was knocked out by the Hyper Beam.

"Great job, Regirock! Return!" Shadow yelled.

Giovanni growled again. This battle was going too fast. "Go! Raikou!"

Shadow paused a moment before pulling out another Master Ball. "Mew! I need your help!"

"Mew!" Mew purred before dodging a Thunder attack from Raikou.

"Raikou! Thunder Fang!" Giovanni ordered.

"Mew! Teleport! Then use Psychic!" Shadow called. Mew teleported out of the way and then hit Raikou with Psychic.

"Raikou! Thunder Fang again!" Giovanni demanded, grinding his teeth.

Raikou bit onto Mew's arm, hurting her with the Thunder Fang attack.

"Mew! Shake him off! Use Seismic Toss!" Shadow yelled.

"Mew can learn Seismic Toss?" Iris whispered to Cilan.

"Apparently." Cilan whispered back.

Favors were in Shadow's odds as the Seismic Toss knocked out Raikou. Both opponents returned their pokemon (Shadow complimenting Mew as he did so) and pulled out their next ones.

Giovanni released Suicune while Shadow released Zapdos.

"Suicune, use Blizzard!" Giovanni ordered.

"Zapdos, dodge and use Thunder!" Shadow commanded.

Zapdos tried to dodge but was frozen solid by the Blizzard.

"Zapdos! Try to break free!" Shadow called.

Zapdos attempted to get out of the ice, but failed.

Shadow sighed. "Return. Go Zekrom! Use Bolt Strike!"

"Suicune! Blizzard again!" Giovanni called.

"Counter with DragonBreath and then use Bolt Strike again!"

The second Bolt Strike was a direct hit and Suicune fainted at the powerful, extra-effective attack.

"Good job, Zekrom! Return!" Shadow said.

"Get back here you useless piece of filth." Giovanni growled.

Shadow glared at him. "We had a deal."

Giovanni smirked and placed his right hand in his pocket. "True. We did."

Iris saw a glint of metal as Giovanni started to withdraw his hand from his pocket.

She covered her mouth to stop from gasping loudly and giving away their position.

It seemed Mewtwo had noticed the gun too, for Shadow was shoved out of the way as a shot rang out.

Shadow looked up from his place on the ground, barely able to register what was going on, but when Mewtwo fell, it was as clear as day what had happened.

"Mewtwo!" Shadow shouted in distress, scurrying over to where Mewtwo lay still and pale.

"_Shadow, I failed you."_ Mewtwo whispered.

"No. No, you saved my life." Shadow said.

"_If I had more than one life to give for you, I would."_ Mewtwo said, reaching a hand up and caressing the face under the mask.

A tear fell on his hand. "Mewtwo, you can't leave me."

"_You have been so brave, Shadow, throughout this whole mission. You've been through more than I can possibly say. I am proud to say I was by your side throughout the whole ideal."_ Mewtwo told him. _"My last request for you is that you finish what we came here to do in whatever way possible. Do it for me, Ash. Do it for me."_ Mewtwo's hand fell to the ground and he was silent.

"No! Mewtwo!" Shadow burst into tears. He didn't realize Mewtwo had just said his name for all to hear.

"Did Mewtwo just call him Ash?" Whispers from the rebels flooded the bushes.

"Nobody's left to protect you, boy. What do you have to say for yourself?" Giovanni snickered, pointing the gun at Shadow.

The boy stood up, wiped his eyes, and called out Mew. He whispered something in her ear and the two teleported away.

"What the… Where'd they go?!" Giovanni shouted.

Suddenly, the gun was yanked out of his hands. Giovanni spun around to find Shadow standing behind him, pointing the gun at him.

"This is for Mewtwo." The boy whispered.

Then, he shot Giovanni in the chest.

**(A/n) Yes, I had Mewtwo die. Someone had to die to protect Ash. If you thought Giovanni wouldn't try something instead of sticking to the deal, you were wrong. (A/n)**


	14. Chapter 13

Gasps filled the clearing as Giovanni's eyes widened and he fell.

One of the grunts said. "He… he killed the boss… HE KILLED THE BOSS!"

The grunts pulled out guns and shot at Shadow, but Mew teleported him out of the way, causing the grunts' bullets to go into each other.

Shadow watched as they all fell before slowly walking to Giovanni and taking the Dark Balls off the criminal leader's belt.

He released the five tired legendary pokemon before walking back to Mewtwo and dropping to his knees beside him.

Slowly, he reached into his bag and, to the rebels' surprise, released every single legendary pokemon he had captured.

"Go. You're safe now to go free." He whispered.

"_I promised you a reward for protecting the legendries and defeating Giovanni, but, alas, even I cannot bring back the dead."_ Arceus said, approaching Shadow after the other legendries had left.

"You brought me back." Shadow said, surprising the rebels again.

"_You still had a spark of life left in you. I'm sorry, but I can't say the same for Mewtwo. I promise, though, that his sacrifice will not be forgotten."_ Arceus told him. _"Any other non-greedy reward, I can give you, but not that."_

Shadow seemed to be thinking. "Can you give me the power to heal someone if they get fatally injured? That way, I'll be able to do something if this happens again."

"_That I can give you."_ Arceus agreed and both glowed as Arceus gave Shadow the power. _"There's also something else I want to give you. I won't tell you what, but you'll figure it out quickly."_

"Okay." Shadow said and both glowed again as Arceus gave him the second power.

"_I must be going now. A lot of reconstruction is needed throughout the world. Hopefully, everyone will be willing to help with that." _Arceus said. _"Goodbye."_

Arceus flew away. Shadow sighed and started digging a grave for Mewtwo.

All the rebels who had witnessed the battle and the aftermath of the battle watched, not quite knowing what he was doing until he dragged Mewtwo into the grave and started pushing the dirt back in.

One by one, they came out of hiding, watching Shadow as he looked for something to mark the grave.

He found a stone and carved some words into it. None of the rebels bothered to read what he wrote.

"Shadow?" Misty spoke at last.

Shadow spun around. "W-what are you doing here?!"

"We meet here on occasion. We just happened to schedule our meeting for today." Iris told him.

"Oh." Shadow mumbled. "Well, at least you brought me a way off the island, right?"

"We actually used our pokemon to get here." A female rebel said.

"Oh." Shadow said, disappointed.

"I have several water-types, Shadow. You can borrow one of mine." Misty said.

"Thank you." Shadow responded. "I really appreciate it."

"First, though, will you please tell us who you are?" Misty added.

Shadow paused for a moment. "In that case, I'd rather stay on the island."

Misty smirked. "Fine then. You can ride Psyduck."

Shadow stopped himself from saying something, choosing instead to mumble. "Fine with me."

"Um… Misty… Psyduck can't swim…" Brock said.

Misty turned to him and put her finger to her lips.

"If you're giving me a pokemon that can't swim, I'd rather stay on the island." Shadow remarked.

"Misty! Don't be mean! Shadow needs a way off the island! We can't just leave him here!" Iris scolded.

Misty rolled her eyes. "I was just trying to get him to tell us who he is."

"I'm Shadow. That's all you need to know." Shadow said quietly.

"Don't push him, Misty. We'll find out eventually." Brock said.

"Fine…" Misty mumbled before calling out her Corsola and Gyarados.

Misty rode Gyarados, while Shadow rode Corsola and the others rode an array of water-type pokemon.

The next few months flew by in a blur. Everyone was focused on getting the world back to how it had been before. Even Shadow and the legendary pokemon helped, but Shadow never gave away his identity.

Then, when everything was back to normal, Shadow disappeared. Rumor had it that he had been last seen in Alto Mare, but nobody saw him ever again.

A few days after Shadow's disappearance, Ash showed up in Pallet Town.

When his friends asked where he'd been and if he knew who Shadow was, he answered that he had been in a three-year coma and asked who Shadow was.

When he heard the news about his mother, he was devastated, but he promised to raise his little half-sister for her.

Despite all the work put into the getting the world back to normal, nothing would ever be the same. Too many people had died, including gym leaders and the champion of Kanto and Johto, Lance.

Still, kids were encouraged to go back out on their pokemon journeys and follow their dreams.

However, the totalitarian world of Team Rocket would never be forgotten.

**(A/n) This is the end of Codename: Shadow. If you want a sequel, I put a poll up for people to vote. I've already got a sequel planned if you want one, but I need support before I post it! (A/n)**


End file.
